The invention discloses a tissue-engineered bone cartilage composite scaffold and a preparation method thereof, belonging to the technical field of biomaterials. The scaffold is of a multilayer integrated structure and comprises a cartilage tissue scaffold layer, a cartilage tissue calcified layer, a porous cell isolation membrane and a bone tissue scaffold layer. The cartilage tissue scaffold layer is inoculated with cartilage cells, and growth factors for promoting formation of cartilage are introduced to promote growth of cartilage cells. Main raw materials like heparan sulfate proteoglycan with good biocompatibility and degradability are selected and used and the method consisting of a cross-linking reaction, freeze drying, directional pore formation, compounding of multiple layers, overall integration and the like are carried out so as to obtain the functionalized multilayer integrated tissue-engineered bone cartilage composite scaffold with good mechanical properties. According to the invention, micro-nano hydroxyapatite crystal, degradable non-stoichiometric polyethylene glycol / poly(epsilon-caprolactone) nanometer coaxial short fiber, RGD-grafted heparan sulfate proteoglycan / oxidized sodium alginate and N-succinyl chitosan are compounded together to prepare the composite scaffold; and the composite scaffold is mainly used for restoration of full-thickness defects of articular cartilage and subchondral bone.